Abstract: This paper researched on the application of the method of independent safety assessment of Signal System for Urban Transit, introduced a method based on the whole lifecycle and risk-oriented of independent safety assessment in detail, compared it with traditional technology oriented method. The proposed method focused on the hazard existing in the operation of Signal System, could control and manage the potential risks. Independent safety assessment (ISA) could help the signal system integrators reduce the risk level as lower as possible, and ensure safety for the operation of Urban Transit Signaling System. This method can be applied to the design and implementation of the Signal System, meet the requirements of safety integrity level proposed by the competent department.